After excoriating Civil War and then reading what Jeff and Shawn have said about it, I do realize that the massive company wide cross-overs are never tales for the ages. Out of all the big cross-overs within a company I think the only one that has any true worth to it is Crisis on Infinite Earths and I'm not sure if that reads all that well on its own. What separates that one from every other massive cross-over is that it changed the DC Universe forever. Infinite Crisis might be next, but as a series it was not that strong, but had the impact of doing the one year later jump which allowed DC to relaunch every single title.
The massive company wide cross-overs almost never work because they are artificial and usually forced. DC has done Millennium, Invasion, War of the Gods and a host of others and all are eminently forgettable. Marvel has Secret Wars, Secret Wars II, Fall of the Mutants, Onslaught, House of M and others and again all forgettable.
The true series for the ages are Watchmen, Dark Knight Returns, New Frontier, League of Extraordinary Gentlemen, Sandman and a select few of others. Many comics have had great runs and wonderful stories, but the true seminal events are few and far between and a cross-over has never been it and still are not it.
For my money the best cross-overs that come to mind is the JLA/Avengers by Busiek and Perez. This was a well done story and a wonderfully illustrated book containing more characters then any other series I can remember. Another great cross-over was the Titans and X-Men by Claremont and Simonson if memory serves. Both series had good solid stories behind the cross-overs.
Essentially cross-overs are the companies way of generating big sales and I think they have to laugh at us for continuing to buy these series and many of the tie in books, when we should be buying Wasteland, Invincible, Local, Mouse Guard, Fable, Human Target, Losers and other great titles.